TY - JOUR AU - Wilson, D. B. PY - 2011 DA - 2011// TI - Microbial diversity of cellulose hydrolysis JO - Curr Opin Microbiol VL - 14 UR - https://doi.org/10.1016/j.mib.2011.04.004 DO - 10.1016/j.mib.2011.04.004 ID - Wilson2011 ER - TY - JOUR AU - Aro, N. AU - Pakula, T. AU - Penttilä, M. PY - 2005 DA - 2005// TI - Transcriptional regulation of plant cell wall degradation by filamentous fungi JO - FEMS Microbiol Rev VL - 29 UR - https://doi.org/10.1016/j.femsre.2004.11.006 DO - 10.1016/j.femsre.2004.11.006 ID - Aro2005 ER - TY - JOUR AU - Lynd, L. R. AU - Laser, M. S. AU - Bransby, D. AU - Dale, B. E. AU - Davison, B. AU - Hamilton, R. PY - 2008 DA - 2008// TI - How biotech can transform biofuels JO - Nat Biotechnol VL - 26 UR - https://doi.org/10.1038/nbt0208-169 DO - 10.1038/nbt0208-169 ID - Lynd2008 ER - TY - JOUR AU - Coradetti, S. T. AU - Craig, J. P. AU - Xiong, Y. AU - Shock, T. AU - Tian, C. AU - Glass, N. L. PY - 2012 DA - 2012// TI - Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi JO - Proc Natl Acad Sci USA VL - 109 UR - https://doi.org/10.1073/pnas.1200785109 DO - 10.1073/pnas.1200785109 ID - Coradetti2012 ER - TY - JOUR AU - Mach-Aigner, A. R. AU - Pucher, M. E. AU - Steiger, M. G. AU - Bauer, G. E. AU - Preis, S. J. AU - Mach, R. L. PY - 2008 DA - 2008// TI - Transcriptional regulation of xyr1, encoding the main regulator of the xylanolytic and cellulolytic enzyme system in Hypocrea jecorina JO - Appl Environ Microbiol VL - 74 UR - https://doi.org/10.1128/AEM.01143-08 DO - 10.1128/AEM.01143-08 ID - Mach-Aigner2008 ER - TY - JOUR AU - Li, Z. AU - Yao, G. AU - Wu, R. AU - Gao, L. AU - Kan, Q. AU - Qu, Y. PY - 2015 DA - 2015// TI - Synergistic and dose-controlled regulation of cellulase gene expression in Penicillium oxalicum JO - PLoS Genet VL - 11 UR - https://doi.org/10.1371/journal.pgen.1005509 DO - 10.1371/journal.pgen.1005509 ID - Li2015 ER - TY - JOUR AU - Xin, Q. AU - Gong, Y. AU - Lv, X. AU - Chen, G. AU - Liu, W. PY - 2013 DA - 2013// TI - Trichoderma reesei histone acetyltransferase Gcn5 regulates fungal growth, conidiation, and cellulase gene expression JO - Curr Microbiol VL - 67 UR - https://doi.org/10.1007/s00284-013-0396-4 DO - 10.1007/s00284-013-0396-4 ID - Xin2013 ER - TY - JOUR AU - Mello-de-Sousa, T. M. AU - Rassinger, A. AU - Derntl, C. AU - Poças-Fonseca, M. J. AU - Mach, R. L. AU - Mach-Aigner, A. R. PY - 2016 DA - 2016// TI - The relation between promoter chromatin status, Xyr1 and cellulase expression in Trichoderma reesei JO - Curr Genom VL - 17 UR - https://doi.org/10.2174/1389202917666151116211812 DO - 10.2174/1389202917666151116211812 ID - Mello-de-Sousa2016 ER - TY - JOUR AU - Antoniêto, A. C. AU - Santos Castro, L. AU - Silva-Rocha, R. AU - Persinoti, G. F. AU - Silva, R. N. PY - 2014 DA - 2014// TI - Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis JO - Fungal Genet Biol VL - 73 UR - https://doi.org/10.1016/j.fgb.2014.10.009 DO - 10.1016/j.fgb.2014.10.009 ID - Antoniêto2014 ER - TY - JOUR AU - Liu, T. AU - Rechtsteiner, A. AU - Egelhofer, T. A. AU - Vielle, A. AU - Latorre, I. AU - Cheung, M. S. PY - 2011 DA - 2011// TI - Broad chromosomal domains of histone modification patterns in C. elegans JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.115519.110 DO - 10.1101/gr.115519.110 ID - Liu2011 ER - TY - JOUR AU - Flaus, A. AU - Owen-Hughes, T. PY - 2011 DA - 2011// TI - Mechanisms for ATP-dependent chromatin remodelling: the means to the end JO - FEBS J VL - 278 UR - https://doi.org/10.1111/j.1742-4658.2011.08281.x DO - 10.1111/j.1742-4658.2011.08281.x ID - Flaus2011 ER - TY - JOUR AU - Ho, L. AU - Crabtree, G. R. PY - 2010 DA - 2010// TI - Chromatin remodelling during development JO - Nature VL - 463 UR - https://doi.org/10.1038/nature08911 DO - 10.1038/nature08911 ID - Ho2010 ER - TY - JOUR AU - Teves, S. S. AU - Weber, C. M. AU - Henikoff, S. PY - 2014 DA - 2014// TI - Transcribing through the nucleosome JO - Trends Biochem Sci VL - 39 UR - https://doi.org/10.1016/j.tibs.2014.10.004 DO - 10.1016/j.tibs.2014.10.004 ID - Teves2014 ER - TY - JOUR AU - Dehé, P. M. AU - Géli, V. PY - 2006 DA - 2006// TI - The multiple faces of Set1 JO - Biochem Cell Biol VL - 84 UR - https://doi.org/10.1139/o06-081 DO - 10.1139/o06-081 ID - Dehé2006 ER - TY - JOUR AU - Kouzarides, T. PY - 2002 DA - 2002// TI - Histone methylation in transcriptional control JO - Curr Opin Genet Dev VL - 12 UR - https://doi.org/10.1016/S0959-437X(02)00287-3 DO - 10.1016/S0959-437X(02)00287-3 ID - Kouzarides2002 ER - TY - JOUR AU - Binda, O. PY - 2013 DA - 2013// TI - On your histone mark, SET, methylate! JO - Epigenetics VL - 8 UR - https://doi.org/10.4161/epi.24451 DO - 10.4161/epi.24451 ID - Binda2013 ER - TY - JOUR AU - Battaglia, S. AU - Lidschreiber, M. AU - Baejen, C. AU - Torkler, P. AU - Vos, S. M. AU - Cramer, P. PY - 2017 DA - 2017// TI - RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases JO - Elife. VL - 6 UR - https://doi.org/10.7554/eLife.25637 DO - 10.7554/eLife.25637 ID - Battaglia2017 ER - TY - JOUR AU - Li, B. AU - Howe, L. AU - Anderson, S. AU - Yates, J. R. AU - Workman, J. L. PY - 2003 DA - 2003// TI - The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II JO - J Biol Chem VL - 278 UR - https://doi.org/10.1074/jbc.M212134200 DO - 10.1074/jbc.M212134200 ID - Li2003 ER - TY - JOUR AU - Smolle, M. AU - Venkatesh, S. AU - Gogol, M. M. AU - Li, H. AU - Zhang, Y. AU - Florens, L. PY - 2012 DA - 2012// TI - Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange JO - Nat Struct Mol Biol VL - 19 UR - https://doi.org/10.1038/nsmb.2312 DO - 10.1038/nsmb.2312 ID - Smolle2012 ER - TY - JOUR AU - Gilbert, T. M. AU - McDaniel, S. L. AU - Byrum, S. D. AU - Cades, J. A. AU - Dancy, B. C. AU - Wade, H. PY - 2014 DA - 2014// TI - A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions JO - Mol Cell Proteom VL - 13 UR - https://doi.org/10.1074/mcp.M114.038224 DO - 10.1074/mcp.M114.038224 ID - Gilbert2014 ER - TY - JOUR AU - Gessaman, J. D. AU - Selker, E. U. PY - 2017 DA - 2017// TI - Induction of H3K9me3 and DNA methylation by tethered heterochromatin factors in Neurospora crassa JO - Proc Natl Acad Sci USA VL - 114 UR - https://doi.org/10.1073/pnas.1715049114 DO - 10.1073/pnas.1715049114 ID - Gessaman2017 ER - TY - JOUR AU - Jamieson, K. AU - McNaught, K. J. AU - Ormsby, T. AU - Leggett, N. A. AU - Honda, S. AU - Selker, E. U. PY - 2018 DA - 2018// TI - Telomere repeats induce domains of H3K27 methylation in Neurospora JO - Elife VL - 7 UR - https://doi.org/10.7554/eLife.31216 DO - 10.7554/eLife.31216 ID - Jamieson2018 ER - TY - JOUR AU - Liu, Y. AU - Liu, N. AU - Yin, Y. AU - Chen, Y. AU - Jiang, J. AU - Ma, Z. PY - 2015 DA - 2015// TI - Histone H3K4 methylation regulates hyphal growth, secondary metabolism and multiple stress responses in Fusarium graminearum JO - Environ Microbiol VL - 17 UR - https://doi.org/10.1111/1462-2920.12993 DO - 10.1111/1462-2920.12993 ID - Liu2015 ER - TY - JOUR AU - Pham, K. T. AU - Inoue, Y. AU - Vu, B. V. AU - Nguyen, H. H. AU - Nakayashiki, T. AU - Ikeda, K. PY - 2015 DA - 2015// TI - MoSET1 (Histone H3K4 methyltransferase in Magnaporthe oryzae) regulates global gene expression during infection-related morphogenesis JO - PLoS Genet VL - 11 UR - https://doi.org/10.1371/journal.pgen.1005385 DO - 10.1371/journal.pgen.1005385 ID - Pham2015 ER - TY - JOUR AU - Gu, Q. AU - Wang, Z. AU - Sun, X. AU - Ji, T. AU - Huang, H. AU - Yang, Y. PY - 2017 DA - 2017// TI - FvSet2 regulates fungal growth, pathogenicity, and secondary metabolism in Fusarium verticillioides JO - Fungal Genet Biol VL - 107 UR - https://doi.org/10.1016/j.fgb.2017.07.007 DO - 10.1016/j.fgb.2017.07.007 ID - Gu2017 ER - TY - JOUR AU - Janevska, S. AU - Baumann, L. AU - Sieber, C. M. K. AU - Münsterkötter, M. AU - Ulrich, J. AU - Kämper, J. PY - 2018 DA - 2018// TI - Elucidation of the two H3K36me3 histone methyltransferases Set2 and Ash1 in Fusarium fujikuroi unravels their different chromosomal targets and a major impact of Ash1 on genome stability JO - Genetics VL - 208 UR - https://doi.org/10.1534/genetics.117.1119 DO - 10.1534/genetics.117.1119 ID - Janevska2018 ER - TY - JOUR AU - Seiboth, B. AU - Karimi, R. A. AU - Phatale, P. A. AU - Linke, R. AU - Hartl, L. AU - Sauer, D. G. PY - 2012 DA - 2012// TI - The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei JO - Mol Microbiol VL - 84 UR - https://doi.org/10.1111/j.1365-2958.2012.08083.x DO - 10.1111/j.1365-2958.2012.08083.x ID - Seiboth2012 ER - TY - JOUR AU - Patananan, A. N. AU - Palmer, J. M. AU - Garvey, G. S. AU - Keller, N. P. AU - Clarke, S. G. PY - 2013 DA - 2013// TI - A novel automethylation reaction in the Aspergillus nidulans LaeA protein generates S-methylmethionine JO - J Biol Chem VL - 288 UR - https://doi.org/10.1074/jbc.M113.465765 DO - 10.1074/jbc.M113.465765 ID - Patananan2013 ER - TY - JOUR AU - Liu, G. AU - Zhang, L. AU - Qin, Y. AU - Zou, G. AU - Li, Z. AU - Qu, Y. PY - 2013 DA - 2013// TI - Long-term strain improvements accumulate mutations in regulatory elements responsible for hyper-production of cellulolytic enzymes JO - Sci Rep. VL - 3 UR - https://doi.org/10.1038/srep01569 DO - 10.1038/srep01569 ID - Liu2013 ER - TY - JOUR AU - Adams, T. H. AU - Boylan, M. T. AU - Timberlake, W. E. PY - 1988 DA - 1988// TI - brlA is necessary and sufficient to direct conidiophore development in Aspergillus nidulans JO - Cell VL - 54 UR - https://doi.org/10.1016/0092-8674(88)90198-5 DO - 10.1016/0092-8674(88)90198-5 ID - Adams1988 ER - TY - JOUR AU - Qin, Y. AU - Bao, L. AU - Gao, M. AU - Chen, M. AU - Lei, Y. AU - Liu, G. PY - 2013 DA - 2013// TI - Penicillium decumbens BrlA extensively regulates secondary metabolism and functionally associates with the expression of cellulase genes JO - Appl Microbiol Biotechnol VL - 97 UR - https://doi.org/10.1007/s00253-013-5273-3 DO - 10.1007/s00253-013-5273-3 ID - Qin2013 ER - TY - JOUR AU - Liu, G. AU - Zhang, L. AU - Wei, X. AU - Zou, G. AU - Qin, Y. AU - Qu, Y. PY - 2013 DA - 2013// TI - Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens JO - PLoS ONE VL - 8 UR - https://doi.org/10.1371/journal.pone.0055185 DO - 10.1371/journal.pone.0055185 ID - Liu2013 ER - TY - JOUR AU - Miller, T. AU - Krogan, N. J. AU - Dover, J. AU - Erdjument-Bromage, H. AU - Tempst, P. AU - Johnston, M. PY - 2001 DA - 2001// TI - COMPASS: a complex of proteins associated with a trithorax-related SET domain protein JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.231473398 DO - 10.1073/pnas.231473398 ID - Miller2001 ER - TY - JOUR AU - Fuchs, S. M. AU - Kizer, K. O. AU - Braberg, H. AU - Krogan, N. J. AU - Strahl, B. D. PY - 2012 DA - 2012// TI - RNA polymerase II carboxyl-terminal domain phosphorylation regulates protein stability of the Set2 methyltransferase and histone H3 di- and trimethylation at lysine 36 JO - J Biol Chem VL - 287 UR - https://doi.org/10.1074/jbc.M111.273953 DO - 10.1074/jbc.M111.273953 ID - Fuchs2012 ER - TY - JOUR AU - Vu, B. V. AU - Pham, K. T. AU - Nakayashiki, H. PY - 2013 DA - 2013// TI - Substrate-induced transcriptional activation of the MoCel7C cellulase gene is associated with methylation of histone H3 at lysine 4 in the rice blast fungus Magnaporthe oryzae JO - Appl Environ Microbiol VL - 79 UR - https://doi.org/10.1128/AEM.02082-13 DO - 10.1128/AEM.02082-13 ID - Vu2013 ER - TY - JOUR AU - Ryu, H. Y. AU - Rhie, B. H. AU - Ahn, S. H. PY - 2014 DA - 2014// TI - Loss of the Set2 histone methyltransferase increases cellular lifespan in yeast cells JO - Biochem Biophys Res Commun VL - 446 UR - https://doi.org/10.1016/j.bbrc.2014.02.061 DO - 10.1016/j.bbrc.2014.02.061 ID - Ryu2014 ER - TY - JOUR AU - Tompa, R. AU - Madhani, H. D. PY - 2007 DA - 2007// TI - Histone H3 lysine 36 methylation antagonizes silencing in Saccharomyces cerevisiae independently of the Rpd3S histone deacetylase complex JO - Genetics VL - 175 UR - https://doi.org/10.1534/genetics.106.067751 DO - 10.1534/genetics.106.067751 ID - Tompa2007 ER - TY - JOUR AU - Keogh, M. C. AU - Kurdistani, S. K. AU - Morris, S. A. AU - Ahn, S. H. AU - Podolny, V. AU - Collins, S. R. PY - 2005 DA - 2005// TI - Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex JO - Cell VL - 123 UR - https://doi.org/10.1016/j.cell.2005.10.025 DO - 10.1016/j.cell.2005.10.025 ID - Keogh2005 ER - TY - JOUR AU - Suzuki, S. AU - Kato, H. AU - Suzuki, Y. AU - Chikashige, Y. AU - Hiraoka, Y. AU - Kimura, H. PY - 2016 DA - 2016// TI - Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw008 DO - 10.1093/nar/gkw008 ID - Suzuki2016 ER - TY - JOUR AU - Li, B. AU - Gogol, M. AU - Carey, M. AU - Lee, D. AU - Seidel, C. AU - Workman, J. L. PY - 2007 DA - 2007// TI - Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin JO - Science VL - 316 UR - https://doi.org/10.1126/science.1139004 DO - 10.1126/science.1139004 ID - Li2007 ER - TY - JOUR AU - Horikoshi, M. AU - Hai, T. AU - Lin, Y. S. AU - Green, M. R. AU - Roeder, R. G. PY - 1988 DA - 1988// TI - Transcription factor ATF interacts with the TATA factor to facilitate establishment of a preinitiation complex JO - Cell VL - 54 UR - https://doi.org/10.1016/0092-8674(88)90118-3 DO - 10.1016/0092-8674(88)90118-3 ID - Horikoshi1988 ER - TY - JOUR AU - Pokholok, D. K. AU - Harbison, C. T. AU - Levine, S. AU - Cole, M. AU - Hannett, N. M. AU - Lee, T. I. PY - 2005 DA - 2005// TI - Genome-wide map of nucleosome acetylation and methylation in yeast JO - Cell VL - 122 UR - https://doi.org/10.1016/j.cell.2005.06.026 DO - 10.1016/j.cell.2005.06.026 ID - Pokholok2005 ER - TY - JOUR AU - Vermeulen, M. AU - Timmers, H. T. M. PY - 2010 DA - 2010// TI - Grasping trimethylation of histone H3 at lysine 4 JO - Epigenomics. VL - 2 UR - https://doi.org/10.2217/epi.10.11 DO - 10.2217/epi.10.11 ID - Vermeulen2010 ER - TY - JOUR AU - Bernstein, B. E. AU - Kamal, M. AU - Lindblad-Toh, K. AU - Bekiranov, S. AU - Bailey, D. K. AU - Huebert, D. J. PY - 2005 DA - 2005// TI - Genomic maps and comparative analysis of histone modifications in human and mouse JO - Cell VL - 120 UR - https://doi.org/10.1016/j.cell.2005.01.001 DO - 10.1016/j.cell.2005.01.001 ID - Bernstein2005 ER - TY - JOUR AU - Vitaliano-Prunier, A. AU - Menant, A. AU - Hobeika, M. AU - Géli, V. AU - Gwizdek, C. AU - Dargemont, C. PY - 2008 DA - 2008// TI - Ubiquitylation of the COMPASS component Swd2 links H2B ubiquitylation to H3K4 trimethylation JO - Nat Cell Biol VL - 10 UR - https://doi.org/10.1038/ncb1796 DO - 10.1038/ncb1796 ID - Vitaliano-Prunier2008 ER - TY - JOUR AU - Morillon, A. AU - Karabetsou, N. AU - Nair, A. AU - Mellor, J. PY - 2005 DA - 2005// TI - Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription JO - Mol Cell VL - 18 UR - https://doi.org/10.1016/j.molcel.2005.05.009 DO - 10.1016/j.molcel.2005.05.009 ID - Morillon2005 ER - TY - JOUR AU - Peláez, I. M. AU - Kalogeropoulou, M. AU - Ferraro, A. AU - Voulgari, A. AU - Pankotai, T. AU - Boros, I. PY - 2010 DA - 2010// TI - Oncogenic RAS alters the global and gene-specific histone modification pattern during epithelial–mesenchymal transition in colorectal carcinoma cells JO - Int J Biochem Cell Biol VL - 42 UR - https://doi.org/10.1016/j.biocel.2010.01.024 DO - 10.1016/j.biocel.2010.01.024 ID - Peláez2010 ER - TY - JOUR AU - Wagner, E. J. AU - Carpenter, P. B. PY - 2012 DA - 2012// TI - Understanding the language of Lys36 methylation at histone H3 JO - Nat Rev Mol Cell Biol VL - 13 UR - https://doi.org/10.1038/nrm3274 DO - 10.1038/nrm3274 ID - Wagner2012 ER - TY - JOUR AU - Xu, L. AU - Xu, L. AU - Zhao, Z. AU - Dong, A. AU - Taconnat, S. L. AU - Renou, J. P. PY - 2008 DA - 2008// TI - Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana JO - Mol Cell Biol VL - 28 UR - https://doi.org/10.1128/MCB.01607-07 DO - 10.1128/MCB.01607-07 ID - Xu2008 ER - TY - JOUR AU - Kizer, K. O. AU - Phatnani, H. P. AU - Shibata, Y. AU - Hall, H. AU - Greenleaf, A. L. AU - Strahl, B. D. PY - 2005 DA - 2005// TI - A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation JO - Mol Cell Biol VL - 25 UR - https://doi.org/10.1128/MCB.25.8.3305-3316.2005 DO - 10.1128/MCB.25.8.3305-3316.2005 ID - Kizer2005 ER - TY - JOUR AU - Eram, M. S. AU - Kuznetsova, E. AU - Li, F. AU - Lima-Fernandes, E. AU - Kennedy, S. AU - Chau, I. PY - 2015 DA - 2015// TI - Kinetic characterization of human histone H3 lysine 36 methyltransferases, ASH1L and SETD2 JO - Biochim Biophys Acta VL - 1850 UR - https://doi.org/10.1016/j.bbagen.2015.05.013 DO - 10.1016/j.bbagen.2015.05.013 ID - Eram2015 ER - TY - JOUR AU - Gregory, G. D. AU - Vakoc, C. R. AU - Rozovskaia, T. AU - Zheng, X. AU - Patel, S. AU - Nakamura, T. PY - 2007 DA - 2007// TI - Mammalian ASH1L is a histone methyltransferase that occupies the transcribed region of active genes JO - Mol Cell Biol VL - 27 UR - https://doi.org/10.1128/MCB.00993-07 DO - 10.1128/MCB.00993-07 ID - Gregory2007 ER - TY - JOUR AU - Li, Y. AU - Zheng, X. AU - Zhang, X. AU - Bao, L. AU - Zhu, Y. AU - Qu, Y. PY - 2016 DA - 2016// TI - The different roles of Penicillium oxalicum LaeA in the production of extracellular cellulase and β-xylosidase JO - Front Microbiol. VL - 7 ID - Li2016 ER - TY - STD TI - National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/. Accessed 05 May 2018. UR - https://www.ncbi.nlm.nih.gov/ ID - ref54 ER - TY - JOUR AU - Larkin, M. A. AU - Blackshields, G. AU - Brown, N. P. AU - Chenna, R. AU - McGettigan, P. A. AU - McWilliam, H. PY - 2007 DA - 2007// TI - Clustal W and Clustal X version 2.0 JO - Bioinformatics. VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm404 DO - 10.1093/bioinformatics/btm404 ID - Larkin2007 ER - TY - JOUR AU - Kumar, S. AU - Stecher, G. AU - Tamura, K. PY - 2016 DA - 2016// TI - MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets JO - Mol Biol Evol VL - 33 UR - https://doi.org/10.1093/molbev/msw054 DO - 10.1093/molbev/msw054 ID - Kumar2016 ER - TY - STD TI - Simple Modular Architecture Research Tool. http://smart.embl-heidelberg.de/. Accessed 05 May 2018. UR - http://smart.embl-heidelberg.de/ ID - ref57 ER - TY - JOUR AU - Schultz, J. AU - Milpetz, F. AU - Bork, P. AU - Ponting, C. P. PY - 1998 DA - 1998// TI - SMART, a simple modular architecture research tool: identification of signaling domains JO - Proc Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.11.5857 DO - 10.1073/pnas.95.11.5857 ID - Schultz1998 ER - TY - STD TI - The Pfam protein families database. http://pfam.xfam.org/. Accessed 05 May 2018. UR - http://pfam.xfam.org/ ID - ref59 ER - TY - JOUR AU - Finn, R. D. AU - Coggill, P. AU - Eberhardt, R. Y. AU - Eddy, S. R. AU - Mistry, J. AU - Mitchell, A. L. PY - 2016 DA - 2016// TI - The Pfam protein families database: towards a more sustainable future JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1344 DO - 10.1093/nar/gkv1344 ID - Finn2016 ER - TY - JOUR AU - Zhang, X. AU - Qu, Y. AU - Qin, Y. PY - 2016 DA - 2016// TI - Expression and chromatin structures of cellulolytic enzyme gene regulated by heterochromatin protein 1 JO - Biotechnol Biofuels VL - 9 UR - https://doi.org/10.1186/s13068-016-0624-9 DO - 10.1186/s13068-016-0624-9 ID - Zhang2016 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Kim, D. AU - Langmead, B. AU - Salzberg, S. L. PY - 2015 DA - 2015// TI - HISAT: a fast spliced aligner with low memory requirements JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3317 DO - 10.1038/nmeth.3317 ID - Kim2015 ER - TY - JOUR AU - Trapnell, C. AU - Williams, B. A. AU - Pertea, G. AU - Mortazavi, A. AU - Kwan, G. AU - Baren, M. J. PY - 2010 DA - 2010// TI - Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1621 DO - 10.1038/nbt.1621 ID - Trapnell2010 ER - TY - JOUR AU - Li, B. AU - Dewey, C. N. PY - 2011 DA - 2011// TI - RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome JO - BMC Bioinform VL - 12 UR - https://doi.org/10.1186/1471-2105-12-323 DO - 10.1186/1471-2105-12-323 ID - Li2011 ER - TY - JOUR AU - Audic, S. AU - Claverie, J. M. PY - 1997 DA - 1997// TI - The significance of digital gene expression profiles JO - Genome Res VL - 7 UR - https://doi.org/10.1101/gr.7.10.986 DO - 10.1101/gr.7.10.986 ID - Audic1997 ER - TY - JOUR AU - Sturn, A. AU - Quackenbush, J. AU - Trajanoski, Z. PY - 2002 DA - 2002// TI - Genesis: cluster analysis of microarray data JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.1.207 DO - 10.1093/bioinformatics/18.1.207 ID - Sturn2002 ER - TY - JOUR AU - Conesa, A. AU - Götz, S. AU - García-Gómez, J. M. AU - Terol, J. AU - Talón, M. AU - Robles, M. PY - 2005 DA - 2005// TI - Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti610 DO - 10.1093/bioinformatics/bti610 ID - Conesa2005 ER - TY - JOUR AU - Fan, X. AU - Lamarre-Vincent, N. AU - Wang, Q. AU - Struhl, K. PY - 2008 DA - 2008// TI - Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn535 DO - 10.1093/nar/gkn535 ID - Fan2008 ER -